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Table 1 Mean estimate of theta estimators for 100x1MB regions for 25 samples

From: Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

 

  Selection

No selection

 

Method

θ w

θ π

θ FL

θ w

θ π

θ FL

Known

649.8

567.1

745.1

930.0

923.5

939.0

ML

648.6

567.9

734.7

932.4

923.7

968.3

GC-hwe 10-6

341.7

372.1

72.2

541.3

640.3

99.9

GC-mLike 10-6

341.7

497.1

32.9

541.3

768.7

44.8

GC-hwe 10-3

556.1

434.7

583.5

784.8

712.4

680.6

GC-mLike 10-3

556.1

598.9

360.4

784.8

897.9

410.1

GC-hwe 10-5

1011.0

594.8

653.7

1244.4

874.1

752.8

GC-mLike 10-5

1011.0

831.8

420.4

1244.4

1131.6

471.8

  1. The genotype likelihoods are simulated with an error rate of 0.5% and an average depth of 2 ×.